OK. This is the OCNMS github repository. It has all of the data, scripts, and other files associated with the OCNMS diving surveys and associated data. It also has a bunch of pdfs and such for reference. These make the repo kind of big but whatever.
I have maintained included all of the data and scripts that were used in the 2018 Shelton et al. paper as well as the stuff we have done more recently. I am planning on doing a big clean out in the not too distant future.... but don't hold your breath.
Big picture, diving data is in /Data. The flat files of most use are in /CSV_2015_on. Markdown documents (in /Markdown Docs) typically call scripts the /R scripts file to do their dirty work.
In general, I try and limit hard coding of paths to one line at the beginning of each document. So if your code isn't working, look there first.
Otherwise, good hunting.